Nanopore Genome Sequencing and Variant Analysis of the Susceptible Candida auris Strain L1537/2020, Salvador, Brazil

Candida auris has been reported worldwide, but only in December 2020, the first strain from a COVID-19 patient in Brazil was isolated. Here, we describe the genome sequence of this susceptible C. auris strain and performed variant analysis of the genetic relatedness with strains from other geographic localities.

in [4]) is part of the South Asia clade (clade I).
Remarkably, the strain was susceptible for all antifungal classes [4]. Whole genome sequencing (WGS) was performed on strain L1537/2020 to enable indepth analysis of its genetic relatedness with publicly available clade I strains. Additionally, WGS of this strain provides genome data of an antifungal susceptible C. auris strain [4,5].
Sequencing was performed on the Oxford Nanopore MinION platform (Oxford Nanopore Technologies, Oxfordshire, UK) using the ligation sequencing kit (SQK-LSK109) and native barcoding kit (EXP- b IQ-TREE generated maximum likelihood phylogenetic analysis using 420,164 SNPs, rooted with strain AR1097 (C. auris clade V). Numbers above branches represent branch lengths interpreted as the numbers of nucleotide substitutions per nucleotide site. The heatmap z-scores and the IQ-Tree branch lengths show that clade I strains were very similar to each other, however, strain L1537/2020 had a longer branch length and a high number of SNPs (1893-2089) compared to other strains in clade I genome assembly was performed using Flye v2.8.2-b1689 (https://github.com/fenderglass/Flye; [7]) with the parameters --nano-raw \ fastq [ --out-dir \ directory [ --genome-size 12.5 m. The assembly resulted in 15 fragments with a total length of 12,687,478 bp (N 50 of 2,134,410 bp; largest fragment 4,519,230 bp) with a mean coverage of 300X. However, when the 7 smaller contigs (range 490-4970 bp) were omitted, the mean coverage was 387X. The 8 large contigs (range 27,834-4,519,230 bp; total length 12,675,277 bp) included the circular mitochondrial genome (27,834 bp; 1000X coverage), the remaining nuclear contigs had a coverage of * 300X.
Although strain L1537/2020 belongs to clade I, it is distantly related to all other representatives of that clade, and in contrast it is susceptible to all common antifungals ( Fig. 1; [4]). Several mutations are reported to play a role in C. auris' antifungal resistance, viz. CIS2 (A27T), ERG3 (W182*, L207I), ERG11 (Y132F, K143R), FKS1 (S639P), MEC3 (A272V), PEA2 (D367V), TAC1B (FS191S, F214S, R495G, S611P), and UPC2 (M365) [3,9,[21][22][23]. None of these mutations are present in the genome of L1537/2020. Nearly all publicly available C. auris genome data was generated by short-read Illumina sequencing [3,9,11,12]. Nonetheless, the relative distant relation of the nanopore-based genome of strain L1537/2020 to other Illumina-sequenced clade I strains cannot be explained by the differences in sequencing technologies. The nanopore flowcell, chemistry and basecalling software used here approaches an accuracy of [ 98%. This means that a SNP precision of [ 99.9% can be achieved in the case of 50X genome coverage [24]. With the 300X coverage for L1537/ 2020 it is unlikely that an erroneous mutation was introduced in the assembly. Hence, further studies are needed to investigate the epidemiological and biological impact of the phenotypic and genotypic differences in L1537/2020 versus its multi-drug resistant siblings within clade I. Astellas, Biotoscana, United Medical, Gilead, MSD and Pfizer. The other authors report no conflict of interest.
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